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 8J5K | pdb_00008j5k

Structural insights into photosystem II supercomplex and trimeric FCP antennae of a centric diatom Cyclotella meneghiniana


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.93 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history. 

Literature

Structural insights into photosystem II supercomplex and trimeric FCP antennae of a centric diatom Cyclotella meneghiniana.

Zhao, S., Shen, L., Li, X., Tao, Q., Li, Z., Xu, C., Zhou, C., Yang, Y., Sang, M., Han, G., Yu, L.J., Kuang, T., Shen, J.R., Wang, W.

(2023) Nat Commun 14: 8164-8164

  • DOI: https://doi.org/10.1038/s41467-023-44055-8
  • Primary Citation Related Structures: 
    8J5K, 8J7Z, 8W4O, 8W4P

  • PubMed Abstract: 

    Diatoms are dominant marine algae and contribute around a quarter of global primary productivity, the success of which is largely attributed to their photosynthetic capacity aided by specific fucoxanthin chlorophyll-binding proteins (FCPs) to enhance the blue-green light absorption under water. We purified a photosystem II (PSII)-FCPII supercomplex and a trimeric FCP from Cyclotella meneghiniana (Cm) and solved their structures by cryo-electron microscopy (cryo-EM). The structures reveal detailed organizations of monomeric, dimeric and trimeric FCP antennae, as well as distinct assemblies of Lhcx6_1 and dimeric FCPII-H in PSII core. Each Cm-PSII-FCPII monomer contains an Lhcx6_1, an FCP heterodimer and other three FCP monomers, which form an efficient pigment network for harvesting energy. More diadinoxanthins and diatoxanthins are found in FCPs, which may function to quench excess energy. The trimeric FCP contains more chlorophylls c and fucoxanthins. These diversified FCPs and PSII-FCPII provide a structural basis for efficient light energy harvesting, transfer, and dissipation in C. meneghiniana.


  • Organizational Affiliation: 
    • Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China.

Macromolecule Content 

  • Total Structure Weight: 1,107.52 kDa 
  • Atom Count: 71,446 
  • Modeled Residue Count: 7,682 
  • Deposited Residue Count: 7,682 
  • Unique protein chains: 28

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PsbAA,
W [auth a]
333Stephanocyclus meneghinianusMutation(s): 0 
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
PsbBB,
X [auth b]
481Stephanocyclus meneghinianusMutation(s): 0 
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
PsbCC,
Y [auth c]
450Stephanocyclus meneghinianusMutation(s): 0 
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
PsbDD,
Z [auth d]
340Stephanocyclus meneghinianusMutation(s): 0 
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
PsbEAA [auth e],
E
75Stephanocyclus meneghinianusMutation(s): 0 
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
PsbFBA [auth f],
F
31Stephanocyclus meneghinianusMutation(s): 0 
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
PsbHCA [auth h],
G [auth H]
65Stephanocyclus meneghinianusMutation(s): 0 
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
PsbIDA [auth i],
H [auth I]
34Stephanocyclus meneghinianusMutation(s): 0 
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
PsbJEA [auth j],
I [auth J]
34Stephanocyclus meneghinianusMutation(s): 0 
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
PsbKFA [auth k],
J [auth K]
37Stephanocyclus meneghinianusMutation(s): 0 
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
PsbLGA [auth l],
K [auth L]
37Stephanocyclus meneghinianusMutation(s): 0 
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
PsbMHA [auth m],
L [auth M]
41Stephanocyclus meneghinianusMutation(s): 0 
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Reference Sequence
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Psb34IA [auth n],
M [auth N]
30Stephanocyclus meneghinianusMutation(s): 0 
Sequence Annotations
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Reference Sequence
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
PsbOJA [auth o],
N [auth O]
248Stephanocyclus meneghinianusMutation(s): 0 
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Reference Sequence
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
PsbQ'KA [auth q],
O [auth Q]
145Stephanocyclus meneghinianusMutation(s): 0 
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Reference Sequence
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
PsbTLA [auth t],
P [auth T]
29Stephanocyclus meneghinianusMutation(s): 0 
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Reference Sequence
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
PsbUMA [auth u],
Q [auth U]
92Stephanocyclus meneghinianusMutation(s): 0 
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Reference Sequence
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
PsbVNA [auth v],
R [auth V]
136Stephanocyclus meneghinianusMutation(s): 0 
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Reference Sequence
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
PsbWOA [auth w],
S [auth W]
50Stephanocyclus meneghinianusMutation(s): 0 
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Reference Sequence
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
PsbXPA [auth x],
T [auth X]
34Stephanocyclus meneghinianusMutation(s): 0 
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Reference Sequence
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
PsbYQA [auth y],
U [auth Y]
33Stephanocyclus meneghinianusMutation(s): 0 
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Reference Sequence
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Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
PsbZRA [auth z],
V [auth Z]
59Stephanocyclus meneghinianusMutation(s): 0 
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Reference Sequence
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Entity ID: 23
MoleculeChains  Sequence LengthOrganismDetailsImage
FCPII-G, fucoxanthin chlorophyll a/c binding proteinBB [auth 0],
SA [auth 5]
169Stephanocyclus meneghinianusMutation(s): 0 
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Reference Sequence
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Entity ID: 24
MoleculeChains  Sequence LengthOrganismDetailsImage
FCPII-H2, fucoxanthin chlorophyll a/c binding proteinCB [auth 2],
TA [auth 7]
164Stephanocyclus meneghinianusMutation(s): 0 
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Reference Sequence
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Entity ID: 25
MoleculeChains  Sequence LengthOrganismDetailsImage
FCPII-H1, fucoxanthin chlorophyll a/c binding proteinDB [auth 1],
UA [auth 6]
164Stephanocyclus meneghinianusMutation(s): 0 
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Reference Sequence
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Entity ID: 26
MoleculeChains  Sequence LengthOrganismDetailsImage
FCPII-I, fucoxanthin chlorophyll a/c binding proteinVA [auth p],
YA [auth P]
214Stephanocyclus meneghinianusMutation(s): 0 
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Reference Sequence
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Entity ID: 27
MoleculeChains  Sequence LengthOrganismDetailsImage
FCPII-K, fucoxanthin chlorophyll a/c binding proteinWA [auth 4],
ZA [auth 9]
153Stephanocyclus meneghinianusMutation(s): 0 
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Reference Sequence
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Entity ID: 28
MoleculeChains  Sequence LengthOrganismDetailsImage
FCPII-J, fucoxanthin chlorophyll a/c binding proteinAB [auth 8],
XA [auth 3]
163Stephanocyclus meneghinianusMutation(s): 0 
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Reference Sequence

Small Molecules

Ligands 16 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
(Subject of Investigation/LOI)

Query on DGD



Download:Ideal Coordinates CCD File
FD [auth C]
GD [auth C]
HD [auth C]
HG [auth c]
IG [auth c]
FD [auth C],
GD [auth C],
HD [auth C],
HG [auth c],
IG [auth c],
JG [auth c],
XD [auth H],
ZG [auth h]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA
(Subject of Investigation/LOI)

Query on CLA



Download:Ideal Coordinates CCD File
AC [auth B]
AD [auth C]
AF [auth b]
AG [auth c]
AJ [auth 6]
AC [auth B],
AD [auth C],
AF [auth b],
AG [auth c],
AJ [auth 6],
AK [auth 4],
AL [auth P],
AM [auth 8],
AN [auth 2],
AO [auth 1],
BC [auth B],
BD [auth C],
BF [auth b],
BG [auth c],
BJ [auth 6],
BK [auth 4],
BL [auth P],
BM [auth 8],
BN [auth 2],
BO [auth 1],
CC [auth B],
CF [auth b],
CG [auth c],
CJ [auth 6],
CK [auth 4],
CM [auth 8],
CN [auth 2],
DC [auth B],
DF [auth b],
DG [auth c],
DJ [auth 6],
DK [auth 4],
DM [auth 8],
DN [auth 2],
EC [auth B],
EF [auth b],
EJ [auth 6],
EK [auth 4],
EM [auth 8],
EN [auth 2],
FC [auth B],
FE [auth W],
FF [auth b],
FI [auth 7],
FJ [auth 6],
FN [auth 2],
GB [auth A],
GC [auth B],
GF [auth b],
GI [auth 7],
GJ [auth 6],
GN [auth 2],
HB [auth A],
HE [auth Z],
HF [auth b],
HH [auth w],
HI [auth 7],
HJ [auth p],
HL [auth 9],
HN [auth 2],
IF [auth b],
II [auth 7],
IJ [auth p],
IK [auth 3],
IL [auth 9],
IM [auth 0],
IN [auth 2],
JD [auth D],
JF [auth b],
JH [auth z],
JI [auth 7],
JJ [auth p],
JK [auth 3],
JL [auth 9],
JM [auth 0],
JN [auth 2],
KB [auth A],
KE [auth a],
KF [auth b],
KI [auth 7],
KJ [auth p],
KK [auth 3],
KL [auth 9],
KM [auth 0],
KN [auth 2],
LD [auth D],
LE [auth a],
LG [auth d],
LI [auth 7],
LJ [auth p],
LK [auth 3],
LL [auth 9],
LM [auth 0],
LN [auth 2],
MD [auth D],
MI [auth 7],
MJ [auth p],
MK [auth 3],
ML [auth 9],
MM [auth 0],
MN [auth 1],
NG [auth d],
NH [auth 5],
NI [auth 7],
NJ [auth p],
NK [auth 3],
NL [auth 9],
NM [auth 0],
OE [auth a],
OG [auth d],
OH [auth 5],
OI [auth 7],
OJ [auth p],
OK [auth 3],
OL [auth 9],
OM [auth 0],
PC [auth C],
PH [auth 5],
PI [auth 7],
PJ [auth p],
PK [auth 3],
PL [auth 9],
PM [auth 0],
QC [auth C],
QH [auth 5],
QI [auth 7],
QK [auth 3],
QL [auth 9],
QM [auth 0],
QN [auth 1],
RB [auth B],
RC [auth C],
RF [auth c],
RH [auth 5],
RI [auth 6],
RK [auth 3],
RM [auth 0],
RN [auth 1],
SB [auth B],
SC [auth C],
SF [auth c],
SH [auth 5],
SK [auth 3],
SM [auth 0],
SN [auth 1],
TB [auth B],
TC [auth C],
TF [auth c],
TH [auth 5],
TK [auth P],
TN [auth 1],
UB [auth B],
UC [auth C],
UF [auth c],
UH [auth 5],
UK [auth P],
UL [auth 8],
UN [auth 1],
VB [auth B],
VC [auth C],
VE [auth b],
VF [auth c],
VH [auth 5],
VI [auth 6],
VJ [auth 4],
VK [auth P],
VL [auth 8],
VN [auth 1],
WB [auth B],
WC [auth C],
WE [auth b],
WF [auth c],
WH [auth 5],
WI [auth 6],
WJ [auth 4],
WK [auth P],
WL [auth 8],
WN [auth 1],
XB [auth B],
XC [auth C],
XE [auth b],
XF [auth c],
XH [auth 5],
XI [auth 6],
XJ [auth 4],
XK [auth P],
XL [auth 8],
XN [auth 1],
YB [auth B],
YC [auth C],
YE [auth b],
YF [auth c],
YI [auth 6],
YJ [auth 4],
YK [auth P],
YL [auth 8],
YN [auth 1],
ZB [auth B],
ZC [auth C],
ZE [auth b],
ZF [auth c],
ZI [auth 6],
ZJ [auth 4],
ZK [auth P],
ZL [auth 8],
ZN [auth 1]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO
(Subject of Investigation/LOI)

Query on PHO



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IB [auth A],
JB [auth A],
ME [auth a],
NE [auth a]
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD
(Subject of Investigation/LOI)

Query on SQD



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MB [auth A]
MC [auth B]
NC [auth B]
OB [auth A]
QE [auth a]
MB [auth A],
MC [auth B],
NC [auth B],
OB [auth A],
QE [auth a],
UE [auth b],
UM [auth 0],
ZH [auth 5]
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
LMG
(Subject of Investigation/LOI)

Query on LMG



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BE [auth M]
BH [auth j]
CE [auth M]
DH [auth m]
EE [auth W]
BE [auth M],
BH [auth j],
CE [auth M],
DH [auth m],
EE [auth W],
EH [auth m],
GE [auth Y],
GH [auth w],
ID [auth C],
IH [auth y],
KC [auth B],
KG [auth c],
OF [auth b],
QD [auth D],
RD [auth D],
SD [auth D],
SG [auth d],
TG [auth d],
TM [auth 0],
UG [auth d],
YH [auth 5],
ZD [auth J]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9
(Subject of Investigation/LOI)

Query on PL9



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NB [auth A],
OD [auth D],
QG [auth d],
RE [auth a]
2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE
C53 H80 O2
FKUYMLZIRPABFK-UHFFFAOYSA-N
LHG
(Subject of Investigation/LOI)

Query on LHG



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AH [auth h]
LC [auth B]
PB [auth A]
PD [auth D]
PF [auth b]
AH [auth h],
LC [auth B],
PB [auth A],
PD [auth D],
PF [auth b],
QB [auth A],
RG [auth d],
SE [auth a],
TD [auth D],
TE [auth a],
UD [auth D],
VG [auth d],
WG [auth d],
YD [auth H]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
A86
(Subject of Investigation/LOI)

Query on A86



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AI [auth 5]
BI [auth 7]
CI [auth 7]
CL [auth P]
EL [auth 9]
AI [auth 5],
BI [auth 7],
CI [auth 7],
CL [auth P],
EL [auth 9],
FK [auth 3],
FL [auth 9],
FM [auth 0],
GK [auth 3],
GL [auth 9],
HM [auth 0],
KH [auth 5],
MH [auth 5],
NN [auth 1],
QJ [auth p],
RL [auth 8],
SI [auth 6],
SJ [auth 4],
SL [auth 8],
TJ [auth 4],
UJ [auth 4],
VM [auth 0],
WM [auth 2],
XM [auth 2]
(3S,3'S,5R,5'R,6S,6'R,8'R)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5,5',6,6',7,8-hexahydro-5,6-epoxy-beta,beta-caroten-3'- yl acetate
C42 H58 O6
SJWWTRQNNRNTPU-XJUZQKKNSA-N
HEM
(Subject of Investigation/LOI)

Query on HEM



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DE [auth V],
FH [auth v],
VD [auth F],
XG [auth f]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
DD6
(Subject of Investigation/LOI)

Query on DD6



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DI [auth 7]
DL [auth P]
EI [auth 7]
HK [auth 3]
ON [auth 1]
DI [auth 7],
DL [auth P],
EI [auth 7],
HK [auth 3],
ON [auth 1],
PN [auth 1],
RJ [auth p],
TI [auth 6],
TL [auth 8],
UI [auth 6],
YM [auth 2],
ZM [auth 2]
(3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol
C40 H54 O3
OGHZCSINIMWCSB-WMTIXGNLSA-N
ET4
(Subject of Investigation/LOI)

Query on ET4



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GM [auth 0],
LH [auth 5]
(1~{R})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E})-3,7,12,16-tetramethyl-18-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15-octaen-17-ynyl]cyclohex-3-en-1-ol
C40 H54 O2
HNYJHQMUSVNWPV-DRCJTWAYSA-N
BCR

Query on BCR



Download:Ideal Coordinates CCD File
AE [auth K]
CD [auth C]
CH [auth k]
DD [auth C]
ED [auth C]
AE [auth K],
CD [auth C],
CH [auth k],
DD [auth C],
ED [auth C],
EG [auth c],
FG [auth c],
GG [auth c],
HC [auth B],
IC [auth B],
JC [auth B],
LB [auth A],
LF [auth b],
MF [auth b],
ND [auth D],
NF [auth b],
PE [auth a],
PG [auth d],
WD [auth H],
YG [auth h]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
OEX
(Subject of Investigation/LOI)

Query on OEX



Download:Ideal Coordinates CCD File
EB [auth A],
IE [auth a]
CA-MN4-O5 CLUSTER
Ca Mn4 O5
SEXWDHMBWJEXOJ-UHFFFAOYSA-N
BCT

Query on BCT



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KD [auth D],
MG [auth d]
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2

Query on FE2



Download:Ideal Coordinates CCD File
FB [auth A],
JE [auth a]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
OC [auth C],
QF [auth c]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Non-standard Monomers  1 Unique
IDChains TypeFormula2D Diagram
UNK
Query on UNK
L-PEPTIDE LINKINGC4 H9 N O2

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.93 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19.2_4158:

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Chinese Academy of SciencesChina--

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-20
    Type: Initial release
  • Version 1.1: 2026-08-12
    Type: Remediation
    Reason: Metalloprotein remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.2: 2026-09-16
    Changes: Data collection, Structure summary
  • Version 1.3: 2026-09-23
    Changes: Data collection